public override string ToString()
{
if (IsPrecursor())
{
return(Resources.Transition_ToString_precursor + GetChargeIndicator(Adduct) +
GetMassIndexText(MassIndex));
}
if (IsCustom())
{
var text = CustomIon.ToString();
// Was there enough information to generate a string more distinctive that just "Ion"?
if (String.IsNullOrEmpty(CustomIon.Name) &&
String.IsNullOrEmpty(CustomIon.NeutralFormula))
{
// No, add mz and charge to whatever generic text was used to describe it
var mz = Adduct.MzFromNeutralMass(CustomIon.MonoisotopicMass);
return(string.Format(@"{0} {1:F04}{2}",
text, mz, GetChargeIndicator(Adduct)));
}
return(text);
}
return(string.Format(@"{0} - {1}{2}{3}{4}",
AA,
IonType.ToString().ToLowerInvariant(),
Ordinal,
GetDecoyText(DecoyMassShift),
GetChargeIndicator(Adduct)));
}
private string GetTextFromMass(double?mass, MassType massType)
{
if (!mass.HasValue)
{
return(string.Empty);
}
var result = mass.Value;
if (!Adduct.IsEmpty)
{
// We want to show this as an m/z value, rounded to a reasonable length
result = Math.Abs(SequenceMassCalc.PersistentMZ(Adduct.MzFromNeutralMass(result, massType)));
}
return(result.ToString(CultureInfo.CurrentCulture));
}
/// <summary>
/// For test purposes
/// </summary>
public static double CalculateIonMz(TypedMass mass, Adduct adduct)
{
return(adduct.MzFromNeutralMass(mass));
}
/// <summary>
/// For test purposes
/// </summary>
public double CalculateIonMz(string desc, Adduct adduct)
{
var mass = CalculateMassFromFormula(desc);
return(adduct.MzFromNeutralMass(mass));
}
public IsotopeDistInfo(MassDistribution massDistribution,
TypedMass monoisotopicMass,
Adduct adduct,
Func <double, double> calcFilterWindow,
double massResolution,
double minimumAbundance)
{
_monoisotopicMass = monoisotopicMass;
_adduct = adduct.Unlabeled; // Don't reapply explicit isotope labels
// Get peak center of mass values for the given resolution
var q1FilterValues = MassDistribution.NewInstance(massDistribution, massResolution, 0).Keys.ToList();
// Find the monoisotopic m/z and make sure it is exactly the expected number
double monoMz = _adduct.MzFromNeutralMass(_monoisotopicMass);
double monoMzDist = monoMz;
int monoMassIndex = 0;
for (int i = 0; i < q1FilterValues.Count; i++)
{
double peakCenterMz = q1FilterValues[i];
double filterWindow = calcFilterWindow(peakCenterMz);
double startMz = peakCenterMz - filterWindow / 2;
double endMz = startMz + filterWindow;
if (startMz < monoMz && monoMz < endMz)
{
monoMzDist = q1FilterValues[i];
q1FilterValues[i] = monoMz;
monoMassIndex = i;
break;
}
}
// Insert a M-1 peak, even if it is not expected in the isotope mass distribution
if (monoMassIndex == 0 && q1FilterValues.Count > 1)
{
// Use the delta from the original distribution monoMz to the next peak
q1FilterValues.Insert(0, monoMz + monoMzDist - q1FilterValues[1]);
monoMassIndex++;
}
if (!q1FilterValues.Any())
{
// This should never happen, but just in case it does happen, we safely exit the constructor
ExpectedPeaks = ImmutableList.Singleton(new MzRankProportion(monoMz, 0, 1.0f));
MonoMassIndex = BaseMassIndex = 0;
return;
}
var signedQ1FilterValues = q1FilterValues.Select(q => new SignedMz(q, adduct.AdductCharge < 0)).ToList();
// Use the filtering algorithm that will be used on real data to determine the
// expected proportions of the mass distribution that will end up filtered into
// peaks
// CONSIDER: Mass accuracy information is not calculated here
var key = new PrecursorTextId(signedQ1FilterValues[monoMassIndex], null, null, ChromExtractor.summed);
var filter = new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, 0, null, null, false, false);
filter.AddQ1FilterValues(signedQ1FilterValues, calcFilterWindow);
var expectedSpectrum = filter.FilterQ1SpectrumList(new[] { new MsDataSpectrum
{
Mzs = massDistribution.Keys.ToArray(), Intensities = massDistribution.Values.ToArray(), NegativeCharge = (adduct.AdductCharge < 0)
} });
int startIndex = expectedSpectrum.Intensities.IndexOf(inten => inten >= minimumAbundance);
if (startIndex == -1)
{
// This can happen if the amino acid modifications are messed up,
// and the peptide mass is negative or something.
ExpectedPeaks = ImmutableList.Singleton(new MzRankProportion(monoMz, 0, 1.0f));
MonoMassIndex = BaseMassIndex = 0;
return;
}
// Always include the M-1 peak, even if it is expected to have zero intensity
if (startIndex > monoMassIndex - 1)
{
startIndex = monoMassIndex - 1;
}
if (startIndex < 0)
{
startIndex = 0;
}
int endIndex = expectedSpectrum.Intensities.LastIndexOf(inten => inten >= minimumAbundance) + 1;
int countPeaks = endIndex - startIndex;
var listProportionIndices = new List <KeyValuePair <float, int> >(countPeaks);
for (int i = 0; i < countPeaks; i++)
{
listProportionIndices.Add(new KeyValuePair <float, int>(
expectedSpectrum.Intensities[i + startIndex], i));
}
// Sort proportions descending.
listProportionIndices.Sort((p1, p2) => Comparer.Default.Compare(p2.Key, p1.Key));
// Set proportions and ranks back in the original locations
var expectedProportionRanks = new KeyValuePair <float, int> [countPeaks];
for (int i = 0; i < countPeaks; i++)
{
expectedProportionRanks[listProportionIndices[i].Value] =
new KeyValuePair <float, int>(listProportionIndices[i].Key, i + 1);
}
MonoMassIndex = monoMassIndex - startIndex;
// Find the base peak and fill in the masses and proportions
var expectedPeaks = new List <MzRankProportion>();
for (int i = 0; i < countPeaks; i++)
{
float expectedProportion = expectedProportionRanks[i].Key;
int rank = expectedProportionRanks[i].Value;
expectedPeaks.Add(new MzRankProportion(q1FilterValues[i + startIndex], rank, expectedProportion));
if (expectedProportion > expectedProportionRanks[BaseMassIndex].Key)
{
BaseMassIndex = i;
}
}
ExpectedPeaks = expectedPeaks;
}